Plant & Animal Genomes XIX Conference Plant & Animal Genomes XIX ConferenceJanuary 15-19, 2011
Town & Country Convention Center
San Diego, CA
Christine Tranchant-Dubreuil , Olga Plechakova , Romain Guyot , Perla Hamon , Claudine Campa , Alexandre de Kochko , Serge Hamon , Valerie Poncet
In the past few years, functional genomics information has been rapidly accumulating on Rubiaceae species and especially on those belonging to the Coffea genus. An increasing number of expressed sequence tag (EST) data and EST- or genomic-derived microsatellite markers have been generated, together with Conserved Ortholog Set (COS) markers. This considerably facilitates comparative genomics or genetic maps based studies through the common use of ortholog loci across different species. Similar genomic information is available for tomato or potato, members of the Solanaceae family. Since both Rubiaceae and Solanaceae belong to the Euasterids I, integration of information on genetic markers would be possible and should lead to more efficient analyses and discovery of key loci involved in important traits such as fruit development, quality or adaptation. Our goal was to develop a comprehensive web data source for integrated information on validated ortholog markers in Rubiaceae.
MOCCAdb (http://moccadb.mpl.ird.fr/) is an interactive online database that manages annotated and/or mapped PCR-based markers defined from ESTs and genomic sequence in Rubiaceae (Plechakova et al., 2009). Marker information was retrieved from 11 published works, and completed with original data validated in the respective laboratories. Markers were checked for redundancy, in vitro tested for cross-amplification and diversity status in up to 38 Rubiaceae. Users can search the database for markers, sequences, maps or information on diversity through multi-option query forms. MoccaDB also includes bioinformatics tools (CMap and BLAST) and hyperlinks to related external data sources (eg : GenBank or SOL Genomic Network database).